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Hi,

You can use fslsplit to get the b0 image (usually  it is the first volume
i.e vol0000.nii.gz). Then use BET on that image, please add the -m option
to have it generate a binary mask.

The next step is to use fslmaths <4D-DTIdata> -mul <Binarymask>  <Output>
to have it masked.

Best,
Khoi

On Thu, Aug 24, 2017 at 6:33 PM, Iris Wei <[log in to unmask]> wrote:

> I think I BET the 4D data, but I can't find a place to change BET's
> setting to not change my volume number of the data. Then how to run BET
> only on the B0 image and used binary mask to mask the whole 4D data?
> Thanks!!
> Miao
>
> 2017-08-24 15:03 GMT-07:00 Khôi Huỳnh <[log in to unmask]>:
>
>> Hi,
>>
>> Then please check your BET procedure. Did you apply BET on 4D data or
>> just the initial B0 image only?  I personally would run BET on the B0 image
>> and use the binary mask to mask the whole 4D data.
>>
>> best,
>> Khoi
>>
>> On Aug 24, 2017, at 5:56 PM, Iris Wei <[log in to unmask]> wrote:
>>
>> Hi Khoi,
>> I just reran dicom2nii again and i found out that the DTI data after
>> conversion is 33 volumes and after eddy it is 33 volumes, but after I ran
>> BET on it, it change to 1 volume.
>> I checked the volume using fslnvols.
>> Miao
>>
>> 2017-08-24 14:35 GMT-07:00 Khôi Huỳnh <[log in to unmask]>:
>>
>>> Hi,
>>>
>>> Could you run it again. Usually, I have no problem from running dcm2nii
>>> to convert the data.
>>>
>>> https://www.nitrc.org/frs/shownotes.php?release_id=1855
>>>
>>> best,
>>> Khoi
>>>
>>> On Aug 24, 2017, at 5:27 PM, Iris Wei <[log in to unmask]> wrote:
>>>
>>> just checked and how come it is one. I used dicom2nii to convert my DWI
>>> data to nifti.
>>> it is one volume?
>>> then how do I fix this?
>>>
>>> 2017-08-24 14:22 GMT-07:00 Khôi Huỳnh <[log in to unmask]>:
>>>
>>>> Hi,
>>>>
>>>> Could you confirm the result of fslnvols <yourdata> is 33 ?
>>>>
>>>> best,
>>>> Khoi
>>>>
>>>> On Aug 24, 2017, at 5:14 PM, Iris Wei <[log in to unmask]> wrote:
>>>>
>>>> And I got my bval and bvec from running dicom2nii. How come it does not
>>>> match my data?
>>>>
>>>> 2017-08-24 14:12 GMT-07:00 Iris Wei <[log in to unmask]>:
>>>>
>>>>> Hi Khoi,
>>>>> Thanks so much for replying.
>>>>> So I attached my bval and bvec with this email and I noticed my bval
>>>>> start from 0 and then 800,...
>>>>> How do I fix this and have DTIFIT to run so that I can continue my
>>>>> analysis?
>>>>> Thanks.
>>>>> Miao
>>>>>
>>>>> 2017-08-24 13:31 GMT-07:00 Khôi Huỳnh <[log in to unmask]>:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> The volume counter in FSLeyes starts at 0. Hence, if your last volume
>>>>>> number is 33, probably that the data has 34 volumes.
>>>>>>
>>>>>> best,
>>>>>> Khoi
>>>>>>
>>>>>> > On Aug 24, 2017, at 4:27 PM, miao Wei <[log in to unmask]>
>>>>>> wrote:
>>>>>> >
>>>>>> > To whom it may concern,
>>>>>> > I submitted a question regarding error message of dtifit yesterday
>>>>>> but was not lucky enough to get a response.
>>>>>> > So I went ahead and checked for my bvec and bval files. Both of
>>>>>> them has 33 entries.
>>>>>> > I used FSLeyes to look at my DTI data and dimension 4 listed as 33
>>>>>> as well. Does this means that I also have 33 volumes?
>>>>>> > If so why when I run DTIFIT it still give me the error message as
>>>>>> 'Errors: data and bvals/bvecs do not contain the same number of entries'.
>>>>>> > I am so confused and could use any hint or help. Thank you!!
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Miao Wei
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Miao Wei
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Miao Wei
>>>
>>>
>>>
>>
>>
>> --
>> Miao Wei
>>
>>
>>
>
>
> --
> Miao Wei
>